[BioC] Nonspecific filtering on Human Gene ST 1.0 Arrays

Benilton Carvalho bcarvalh at jhsph.edu
Fri Nov 27 17:01:29 CET 2009


This is possibly due to my email about one week ago when I suggested  
that:

annotation(OligoEset) <- "hugene10sttranscriptcluster.db"

would suffice. But apparently the ".db" bit isn't required.

b

On Nov 27, 2009, at 1:51 PM, Javier Pérez Florido wrote:

> Martin Morgan escribió:
>> Javier Pérez Florido wrote:
>>
>>> Martin Morgan escribió:
>>>
>>>> "James W. MacDonald" <jmacdon at med.umich.edu> writes:
>>>>
>>>>
>>>>
>>>>> Hi Javier,
>>>>>
>>>>> Javier Pérez Florido wrote:
>>>>>
>>>>>
>>>>>> Dear list,
>>>>>> I've tried to use the nsFilter function from genefilter package  
>>>>>> to
>>>>>> perform nonspecific filtering on a Human Gene ST 1.0 dataset.
>>>>>> The expression set has the hugene10sttranscriptcluster.db  
>>>>>> annotation
>>>>>> package, but when nsFilter is applied:
>>>>>> nsFilter(subEset,var.cutoff=0.5) # Removes AFFX genes, those  
>>>>>> without
>>>>>> EntrezGene IDs, etc
>>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) :
>>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found
>>>>>>
>>>>>>
>>>>> annotation(subEset) <- "hugene10sttranscriptcluster"
>>>>>
>>>>>
>>>> genefilter 1.28.1 should work for both
>>>> "hugene10sttranscriptcluster.db" and "hugene10sttranscriptcluster".
>>>>
>>>>
>>> I've checked that it only works when
>>>
>>> annotation(subEset) <- "hugene10sttranscriptcluster"
>>>
>>
>> Can you be more specific? The previous error was
>>
>>
>>>>>> Error is do.call(paste(chip, "_dbconn", sep = ""), list()) :
>>>>>> "hugene10sttranscriptcluster.db_dbconn" cannot be found
>>>>>>
>>
>> if you see the same message then can you confirm that you have
>> genefilter 1.28.1 installed? If there is a different error then can  
>> you
>> please provide me with that? I do not have a 'real' hugene eset with
>> which to work.
>>
>> Martin
>>
> Dear Martin,
> I've updated genefilter from version 1.28.0 to version 1.28.1. When  
> I'm
> trying to use genefilter
>
> annotation(OligoEset) <- "hugene10sttranscriptcluster.db"
> OligoEset<-nsFilter(OligoEset, require.entrez=TRUE,require.GOBP=TRUE,
> remove.dupEntrez=TRUE,
> var.func=IQR,var.cutoff=varCutoff,filterByQuantile=TRUE,
> feature.exclude="petete")$eset
> Error in get(paste(data, centID, sep = "")) :
>  object 'hugene10sttranscriptcluster.dbENTREZID' not found
>
> However, if
> annotation(OligoEset) <- "hugene10sttranscriptcluster"
>
> nsFilter works well.
>
> Hope this helps,
> Javier
>
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252
> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C
> [5] LC_TIME=Spanish_Spain.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pd.hugene.1.0.st.v1_3.0.0
> oligo_1.10.0                         preprocessCore_1.8.0
> [4] oligoClasses_1.8.0
> genefilter_1.28.1                    GOstats_2.12.0
> [7] graph_1.24.0
> Category_2.12.0                      limma_3.2.1
> [10] hugene10sttranscriptcluster.db_4.0.1
> org.Hs.eg.db_2.3.6                   RSQLite_0.7-3
> [13] DBI_0.2-4
> AnnotationDbi_1.8.0                  vsn_3.14.0
> [16] Biobase_2.6.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.18.0 affy_1.24.0       affyio_1.14.0
> annotate_1.24.0   Biostrings_2.14.0 GO.db_2.3.5       grid_2.10.0
> [8] GSEABase_1.8.0    IRanges_1.4.0     lattice_0.17-26
> RBGL_1.20.0       splines_2.10.0    survival_2.35-7   tools_2.10.0
> [15] XML_2.6-0         xtable_1.5-5
>>
>>> Javier
>>>
>>>
>>>
>>>> Martin
>>>>
>>>>
>>>>
>>>>> Should do the trick.
>>>>>
>>>>> Best,
>>>>>
>>>>> Jim
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> Maybe nsFilter is not built for this kind of microarrays,  
>>>>>> although
>>>>>> varFilter,from the same package, works, because it makes use of  
>>>>>> the
>>>>>> expression values only.
>>>>>> I've made some search on Google, but no success. I can write a
>>>>>> function that removes the different control genes in Human Gene
>>>>>> (AFFX, spike, neg_control,pos_control,etc) and those without
>>>>>> EntrezGene ID, but wanted to know if there is a function that  
>>>>>> handle
>>>>>> this for this kind of microarrays.
>>>>>> Thanks,
>>>>>> Javier
>>>>>> sessionInfo()
>>>>>> R version 2.10.0 (2009-10-26)
>>>>>> i386-pc-mingw32
>>>>>> locale:
>>>>>> [1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252   
>>>>>> [3]
>>>>>> LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                 [5]
>>>>>> LC_TIME=Spanish_Spain.1252  attached base packages:
>>>>>> [1] stats     graphics  grDevices utils     datasets  methods    
>>>>>> base
>>>>>> other attached packages:
>>>>>> [1] Matrix_0.999375-31                   lattice_0.17-26
>>>>>> [3] ALL_1.4.7                            genefilter_1.28.0
>>>>>> [5] pd.hugene.1.0.st.v1_3.0.0            Category_2.12.0
>>>>>> [7] KEGG.db_2.3.5
>>>>>> hugene10sttranscriptcluster.db_4.0.1
>>>>>> [9] org.Hs.eg.db_2.3.6                   RSQLite_0.7-3
>>>>>> [11] DBI_0.2-4                            oligo_1.10.0
>>>>>> [13] preprocessCore_1.8.0                 oligoClasses_1.8.0
>>>>>> [15] GSEABase_1.8.0                       graph_1.24.0
>>>>>> [17] annotate_1.24.0                      AnnotationDbi_1.8.0
>>>>>> [19] Biobase_2.6.0                     loaded via a namespace  
>>>>>> (and
>>>>>> not attached):
>>>>>> [1] affxparser_1.18.0 affyio_1.14.0     Biostrings_2.14.0
>>>>>> grid_2.10.0     [5] IRanges_1.4.0     RBGL_1.20.0
>>>>>> splines_2.10.0    survival_2.35-7 [9] tools_2.10.0      XML_2.6-0
>>>>>> xtable_1.5-5    >
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
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>>>>>>
>>>>>>
>>>>
>>>>
>>
>>
>>
>
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